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PubMed1996

Automated particle classification based on digital acquisition and analysis of flow cytometric pulse waveforms.

In flow cytometry, the typical use of front-end analog processing limits the pulse waveform features that can be measured to pulse integral, height, and width. Direct digitizing of the waveforms provides a means for the extraction of additional features, for example, pulse skewness and kurtosis, and Fourier properties. In this work, we have first demonstrated that the Fourier properties of the pulse can be employed usefully for discrimination between different types of cells that otherwise cannot be classified by using only time-domain features of the pulse. We then implemented and evaluated automatic procedures for cell classification based on neural networks. We established that neural networks could provide an efficient means of classification of cell types without the need for user interaction. The neural networks were also employed in an innovative manner for analysis of the digital flow cytometric data without feature extraction. The performance of the neural networks was compared with that of a more conventional means of classification, the K-means clustering algorithm. Neural networks can be realized in hardware, and this, in addition to their highly parallel architecture, makes them an important potential part of real-time analysis systems. These results are discussed in terms of the design of a real-time digital data acquisition system for flow cytometry.

Animals↗
PubMed1993

Quantitative analysis of gel electrophoretograms by image analysis and least squares modeling.

A computer-aided quantitative method for a complex analysis of gel electrophoretograms is presented. The analysis consists of several steps: (i) determination of the background image by methods of mathematical morphology and its subtraction from the gel image, (ii) selection of an appropriate part of the gel lane including curved lanes and lanes with a nonuniform width, (iii) computation of the lane densitogram by averaging several lane-parallel scans, (iv) decomposition of the lane densitogram into component bands using a data selecting algorithm and Marquardt's minimizer. Several different functions for component bands are utilized. It is shown that the densitogram can be decomposed into component bands with reasonable accuracy only if an appropriate model function is chosen. The algorithms are tested on several different gel electrophoretograms which show typical features as a nonuniform background, curved lanes, an asymmetrical band shape and a superposition of small bands on the shoulders of big ones. It is shown that overlapped bands are best approximated by an asymmetrical Gausian curve and an asymmetrical Gauss-Cauchy function. Linear response to the serial dilution of the protein sample is tested.

DNA, Bacterial↗
PubMed2003

Rigid-body dynamics in the isothermal-isobaric ensemble: a test on the accuracy and computational efficiency.

We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermal-isobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL.

Journal Article↗
PubMed2003

Molecular computing revisited: a Moore's Law?

Moore's Law states that the processing power of microchips doubles every one to two years. This observation might apply to the nascent field of molecular computing, in which biomolecules carry out logical operations. Incorporation of new technologies that improve sensitivity and throughput has increased the complexity of problems that can be addressed. It is an ultimate goal for molecular computers to use the full potential of massive parallelism.

Algorithms↗
PubMed1989

The clinical utility of renal concentrating capacity in polycystic kidney disease.

We studied 177 adult nonazotemic subjects with autosomal dominant polycystic kidney disease (ADPKD) and 123 unaffected family members (NADPKD). In order to assess the factors influencing renal concentrating capacity maximal urinary osmolality (UOsm) after overnight water deprivation and vasopressin was measured. UOsm was reduced in ADPKD (680 +/- 14) compared to NADPKD subjects (812 +/- 13 mOsm/kg). A greater severity of the architectural abnormality as assessed by cyst number and size and remaining volume of normal parenchyma was associated with a greater impairment of renal concentrating capacity. The concentrating defect was present in the youngest ADPKD subjects and the rate of decline of concentrating capacity with age in ADPKD paralleled that in NADPKD subjects. Based on the initial 135 subjects studied, we developed an algorithm for diagnostic screening for ADPKD utilizing blood pressure, serum creatinine and UOsm designed to maximize sensitivity. When applied to a subsequent population of 165 adults, 121 with ADPKD and 44 unaffected relatives, this algorithm would have spared 20% of unaffected subjects from the cost of ultrasound while failing to detect less than 2% of affected subjects. This simple protocol thus offers a rapid and inexpensive way to screen for ADPKD.

Adult↗
PubMed1982

Neural networks and physical systems with emergent collective computational abilities.

Computational properties of use of biological organisms or to the construction of computers can emerge as collective properties of systems having a large number of simple equivalent components (or neurons). The physical meaning of content-addressable memory is described by an appropriate phase space flow of the state of a system. A model of such a system is given, based on aspects of neurobiology but readily adapted to integrated circuits. The collective properties of this model produce a content-addressable memory which correctly yields an entire memory from any subpart of sufficient size. The algorithm for the time evolution of the state of the system is based on asynchronous parallel processing. Additional emergent collective properties include some capacity for generalization, familiarity recognition, categorization, error correction, and time sequence retention. The collective properties are only weakly sensitive to details of the modeling or the failure of individual devices.

Animals↗
PubMed2000

Reconstruction of two- and three-dimensional images from synthetic-collimator data.

A novel SPECT collimation method, termed the synthetic collimator, is proposed. The synthetic collimator employs a multiple-pinhole aperture and a high-resolution detector. The problem of multiplexing, normally associated with multiple pinholes, is reduced by obtaining projections at a number of pinhole-detector distances. Projections with little multiplexing are collected at small pinhole-detector distances and high-resolution projections are collected at greater pinhole-detector distances. These projections are then reconstructed using the ML-EM algorithm. It is demonstrated through computer simulations that the synthetic collimator has superior resolution properties to a high-resolution parallel-beam (HRPB) collimator and a specially built ultra-high-resolution parallel-beam (UHRPB) collimator designed for our 0.38-mm pixel CdZnTe detectors. It is also shown that reconstructing images in three dimensions is superior to reconstructing them in two dimensions. The advantages of a high-resolution synthetic collimator over the parallel-hole collimators are apparently reduced in the presence of statistical noise. However, a high-sensitivity synthetic collimator was designed which again shows superior properties to the parallel-hole collimators. Finally, it is demonstrated that, for the cases studied, high-resolution detectors are necessary for the proper functionality of the synthetic collimator.

Algorithms↗
PubMed2002

Computational reconstruction of images from holograms.

The equations to reconstruct an image plane from a hologram are developed. This development is carried out for planes parallel to the hologram, which allows fast computation through the use of fast Fourier transforms. Algorithms for a digital computer are developed so images can be reconstructed, both with and without the Fresnel approximation, from a digitized hologram without the need for three-dimensional optical reconstruction equipment. Examples of holographically recorded images of marine micro-organisms are shown. A computational method for counting the number of micro-organisms in the holographically recorded volume is developed, and an example is provided.

Journal Article↗
PubMed2003

Two-dimensional correlation analysis in application to a kinetic model of parallel reactions.

By applying generalized two-dimensional (2D) correlation analysis as reported by Noda, we have systematically studied a kinetic model of parallel reactions. Given the related rate constants and absorption coefficients, the correlation between reactant and products are analyzed. The reactant-reactant, reactant-product, and product-product pairs are found to be synchronously correlated, and their intensities increase with increase of the rate constant and the absorption coefficient. On the other hand, only the reactant-product pairs show in the asynchronous spectra. Their intensities also depend proportionally on the rate constant and the absorption coefficient. The influence of signal-to-noise ratio (S/N) and overlapped spectra are further discussed. The resulting synchronous and asynchronous correlation spectra for the kinetic model appear to be weakly influenced by poor quality of the signal when the reference spectrum is set at zero. The ratio of asynchronous to synchronous correlation intensity yields a coherence spectrum. This spectrum remains a constant intensity for all the correlated peaks, being free from the influence of rate constant and absorption coefficient as well as being weakly disturbed by a small S/N ratio. It also provides a way to evaluate the extent of spectral overlap between two peaks. The coherence spectrum is useful to characterize the type of parallel reactions.

Algorithms↗
PubMed2002

[Effectiveness of endovideosurgical technology in diagnosis and treatment of patient with hemoblastoses].

Results of using endovideosurgical technology for diagnosis and treatment of hematological diseases in 123 patients are described. It was shown that laparoscopy is highly effective parallel with ultrasound examination and tomography in a complex diagnostic program. Using the developed diagnostic algorithm was shown to be very expedient for making primary diagnosis, recurrent diseases and control of the effectiveness of chemotherapy. Endovideosurgical interventions were shown to be less invasive and safe in hematological patients. Laparoscopy is an alternative to diagnostic laparotomy which is often used in this group of patients.

Adult↗
PubMed1997

Dynamic three-dimensional echocardiography: a new era in ultrasound technology.

The use of noninvasive methods to visualise the heart has had an extraordinary development over the last decade, with echocardiography demonstrating a particularly fast growth. Despite its unquestionable role in the diagnosis of heart disease and in the management of cardiac patients, it does have some limitations, both in the morphological visualisation, as well as in the functional assessment of the heart, such as blood flow, quantification of intracardiac volumes, etc. The recent development of dynamic three-dimensional (3D) echocardiography from two dimensional images has opened new perspectives in the study of cardiac pathophysiology. There are basically two methods of displaying three dimensional data sets: (1) a two-dimensional display from individual selected cut planes (any-plane echocardiography) or from parallel short axis cuts; (2) a volume rendered technique: from any defined cut plane, different algorithms are applied to represent the information in space. There are several potential clinical applications of 3D such as the measurement and serial follow-up of left ventricular volumes; in valvular heart disease (the abnormalities can be delineated more precisely and in greater detail than conventional imaging, including a detailed definition of mitral apparatus in mitral stenosis), in mitral valve prolapse both leaflets can be seen from the left atrial view and in endocarditis it can aid in deciding when and how to intervene; in complex congenital heart disease, such as reconstruction of double outlet right ventricle, left-sided obstructive and regurgitant lesions and subaortic obstructive cases, in atrial and ventricular septal defects, displaying size, geometry and relationships to other structures; another expression of cardiac disorders are blood flow disturbances (visualisation of flows in 3D could allow a better qualitative and quantitative assessment of their size and severity; the pictures so far generated allow a good perception of the size and shape of mitral, aortic and tricuspid regurgitation jets, by examining them from a new perspective, it also has the potential to display the flow convergence zone and quantify the regurgitant volume). Recent studies have clearly demonstrated the feasibility of performing three-dimensional imaging in a variety of cardiac diseases, but continued development of ultrasound technology must be made to improve better image resolution. The prolonged acquisition time is the most important limiting factor that currently restricts the routine use of 3D echocardiography. The development of faster computers will shorten the time needed for image acquisition, postprocessing, and data analysis, contributing to the goal of easy access and wide use. With improvements in computer technology and production of interactive software, 3D echocardiography will provide a dynamic view of the surgical anatomy of the heart. Thus, the three-dimensional reconstruction concept has the potential to and diagnostic assessment of cardiac pathology in every facet.

Cardiovascular Diseases↗
PubMed2002

A parallel mixture of SVMs for very large scale problems.

Support vector machines (SVMs) are the state-of-the-art models for many classification problems, but they suffer from the complexity of their training algorithm, which is at least quadratic with respect to the number of examples. Hence, it is hopeless to try to solve real-life problems having more than a few hundred thousand examples with SVMs. This article proposes a new mixture of SVMs that can be easily implemented in parallel and where each SVM is trained on a small subset of the whole data set. Experiments on a large benchmark data set (Forest) yielded significant time improvement (time complexity appears empirically to locally grow linearly with the number of examples). In addition, and surprisingly, a significant improvement in generalization was observed.

Algorithms↗
PubMed1998

Astigmatic single photon emission computed tomography imaging with a displaced center of rotation.

A filtered backprojection algorithm is developed for single photon emission computed tomography (SPECT) imaging with an astigmatic collimator having a displaced center of rotation. The astigmatic collimator has two perpendicular focal lines, one that is parallel to the axis of rotation of the gamma camera and one that is perpendicular to this axis. Using SPECT simulations of projection data from a hot rod phantom and point source arrays, it is found that a lack of incorporation of the mechanical shift in the reconstruction algorithm causes errors and artifacts in reconstructed SPECT images. The collimator and acquisition parameters in the astigmatic reconstruction formula, which include focal lengths, radius of rotation, and mechanical shifts, are often partly unknown and can be determined using the projections of a point source at various projection angles. The accurate determination of these parameters by a least squares fitting technique using projection data from numerically simulated SPECT acquisitions is studied. These studies show that the accuracy of parameter determination is improved as the distance between the point source and the axis of rotation of the gamma camera is increased. The focal length of the focal line perpendicular to the axis of rotation is determined more accurately than the focal length to the focal line parallel to this axis.

Algorithms↗
PubMed2001

Rebinning-based algorithms for helical cone-beam CT.

Several image reconstruction algorithms based on rebinning have been proposed recently for helical cone-beam CT. These algorithms separate the 3D reconstruction into a set of independent 2D reconstructions for a set of surfaces: planar or non-planar surfaces are defined and then reconstructed using 2D filtered backprojection from a 2D fan-beam or parallel-beam set of data estimated from the cone-beam (CB) measurements. The first part of this paper presents a unified derivation of rebinning algorithms for planar and non-planar surfaces. An integral equation is derived for the surface allowing the best rebinning and an iterative algorithm converging to the solution of that equation is given. The second part presents an efficient method to correct the residual reconstruction artefacts observed with rebinning algorithms when the cone-angle is too large for the required accuracy. This correction algorithm involves a CB backprojection and the reconstruction time is slightly longer than for the zero-boundary (ZB) method.

Algorithms↗
PubMed1999

Parallel image segmentation using the L4 network.

Each processing element in the outer plexiform layer of the fly's (Musca domestica) compound eye has a single copy of a monopolar cell called L4 whose function is still unknown. This paper proposes that L4 acts as an image segmentor receiving data from the L1 and L2 cell layer above it. The photoreceptor terminals R1 through R6 and L1 and L2 form a cartridge with shunting current inhibition that enhances contrast at the first synaptic contact. The photoreceptors feeding their respective terminals share a common optical axis. What was realized for this entire structure that led up to and included L1 and L2, was that it forms a single processing element which outputs a weighted function based on current shunting between the photoreceptor axon terminals around L1 and L2. Thus the basic biological 'algorithm' that this paper proposes for L1 and L2 involves a summation of the differences between a central reference cell (referred to as Rref) and the six neighboring photoreceptor terminals R1-R6 within the cartridge of L1 and L2. Simulation implementing this simple algorithm on a hexagonal packed matrix in Matlab, suggest that objects with even small differences in intensity with the background, can readily be distinguished from the background. This high pass filter biological model allows edge detection and segmentation, independent of scale in a parallel, modular fashion. Implementation of such a biological algorithm using analog circuitry forms a preprocessing unit that introduces virtually no delay in the processing of image information, in comparison to present DSP techniques, that require iterative approaches and costly computing time.

Algorithms↗
PubMed2002

Proteins wriggle.

We propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model, when proteins fold under physiological conditions, their backbone dihedral angles change synchronously in groups of four or more to avoid steric clashes and respect the kinematic conservation laws. They wriggle; they do not thrash. We describe a simple algorithm that can be used to incorporate wriggling in Monte Carlo simulations of protein folding. We have tested this wriggling algorithm against a code in which the dihedral angles are varied independently (thrashing). Our standard of success is the average root-mean-square distance (rmsd) between the alpha-carbons of the folding protein and those of its native structure. After 100,000 Monte Carlo sweeps, the relative decrease in the mean rmsd, as one switches from thrashing to wriggling, rises from 11% for the protein 3LZM with 164 amino acids (aa) to 40% for the protein 1A1S with 313 aa and 47% for the protein 16PK with 415 aa. These results suggest that wriggling is useful and that its utility increases with the size of the protein. One may implement wriggling on a parallel computer or a computer farm.

Algorithms↗
PubMed1998

Molecular evidence for parallel evolution of adaptive syndromes in fig-breeding Lissocephala (Drosophilidae).

Afrotropical Lissocephala (Drosophilidae) breed strictly in syconia (figs) of Ficus (Moraceae) and have accordingly evolved specific features including modified female and eggshell morphologies, ovipositing, larval foraging, and mating behaviors. These various traits may exist as two or three alternative states. Each species displays a specific suite of traits so closely coordinated with one another that alternative states of the overall suites of traits can be seen as "adaptive syndromes." Three clear-cut adaptive syndromes can be recognized while two taxonomic lineages (juncta and sanu species groups) are traditionally accepted on the basis of male terminalia. A crucial evolutionary question results from the consideration that ecological clusters and taxonomic groups have conflicting compositions: the three syndromes are found in the juncta group while two of them occur in the sanu group. To resolve this conflict, we present molecular data which provide a robust phylogeny: mitochondrial DNA (12S + 16S ribosomal DNA and cytochrome b) sequence data are in agreement with one another regardless of the algorithm used. All molecular data consistently support male terminalia dichotomy. Such a level of consistency unambiguously indicates that parallel evolution of adaptive syndromes occurred. Thus, homoplasy may affect morphological and behavioral traits concomitantly when these are involved in a network of functional relationships.

Adaptation, Physiological↗